High speed fluorescence microscopy has created incredible opportunities to tag nano-/micro-scale biological agents (proteins, organelles, vesicles, etc) and track them dynamically. With opportunities comes challenges. With most of these microscopy methods, other biological entities in the environment (membranes, microtubules, actin networks) cannot be visualized simultaneously. Can we use the dynamic observations from the agents of interest to infer the structure of these other biological entities or at least not corrupt our inference of the dynamics of those original agents? In this talk, I will discuss two such biological challenges along with particular data sets: 1) Molecular motor/cargo complexes (agents) and their interaction with un-visualized microtubules. 2) Tracer particles interacting with membranes (cellular, nuclear, etc ).